Changeset 567b7f for molecuilder/src/atom.hpp

Timestamp:

Oct 7, 2009, 1:11:28 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

0cd3b2

Parents:

8ffe32

git-author:

Frederik Heber <heber@…> (10/07/09 12:14:15)

git-committer:

Frederik Heber <heber@…> (10/07/09 13:11:28)

Message:

In molecule::OutputTrajectories() ActOnAllAtoms() with new function atom::OutputTrajectory() is used.

For this to work, I had to change the Trajectory struct that was so far included in molecule.hpp to be incorporated directly into the class atom.
NOTE: This incorporation is incomplete and a ticket (#34) has been filed to remind of this issue.
However, the trajectory is better suited to reside in atom anyway and was probably just put in molecule due to memory prejudices against STL vector<>.
Functions in molecule.cpp, config.cpp, molecule_geometry.cpp and molecule_dynamics.cpp were adapted (changed from Trajectories[atom *] to atom *->Trajectory).
And the atom pointer in the Trajectory structure was removed.

File:

• molecuilder/src/atom.hpp (modified) (4 diffs)

molecuilder/src/atom.hpp

@@ -18 +18 @@
 
 #include <iostream>
+#include <vector>
 
 #include "element.hpp"
@@ -28 +29 @@
 class atom : public TesselPoint {
   public:
-    Vector x;       //!< coordinate array of atom, giving position within cell
-    Vector v;       //!< velocity array of atom
+    struct
+    {
+      vector<Vector> R;  //!< position vector
+      vector<Vector> U;  //!< velocity vector
+      vector<Vector> F;  //!< last force vector
+    } Trajectory;
+
+    Vector x;       //!< coordinate vector of atom, giving last position within cell
+    Vector v;       //!< velocity vector of atom, giving last velocity within cell
+    Vector F;       //!< Force vector of atom, giving last force within cell
     element *type;  //!< pointing to element
     atom *previous; //!< previous atom in molecule list
@@ -51 +60 @@
   virtual ~atom();
 
-  bool Output(int ElementNo, int AtomNo, ofstream *out, const char *comment = NULL) const;
-  bool Output(int *ElementNo, int *AtomNo, ofstream *out, const char *comment = NULL);
+  bool Output(ofstream *out, int ElementNo, int AtomNo, const char *comment = NULL) const;
+  bool Output(ofstream *out, int *ElementNo, int *AtomNo, const char *comment = NULL);
   bool OutputXYZLine(ofstream *out) const;
+  bool OutputTrajectory(ofstream *out, int *ElementNo, int *AtomNo, int step) const;
   void EqualsFather ( atom *ptr, atom **res );
   void CorrectFather();
@@ -66 +76 @@
 };
 
+
 ostream & operator << (ostream &ost, const atom &a);